Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	225,004	G→T	E31* (GAA→TAA)	murQ →	N‑acetylmuramic acid 6‑phosphate etherase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	225,004	0	G	T	100.0%	75.7 / NA	27	E31* (GAA→TAA)	murQ	N‑acetylmuramic acid 6‑phosphate etherase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base T (16/11);  total (16/11)

GCCGAATGATACATTTGATTTTCAAAAAACTAGGGAGTGTAAGAAGTGATGGAAAATAGTACGACCGAAGCGCGTAATGAAGCGACGATGCATCTTGATGAAATGACTGTGGAAGAGGCTTTAATTACGATGAATAAAGAAGATCAGCAAGTCCCGTTAGCAGTTCGAAAGGCAATACCACAATTGACAAAAGTAATTAAAAAAACAATTGCACAGTATAAAAAGGGTGGACGATTGATTTATATCGGTGCAGGTACAAGTGGAAGGTTGGGTGTC  >  USA300TCH1516_ALE/224866‑225141                                                                                                                                           |                                                                                                                                          gCCGAATGATACATTTGATTTTCAAAAAACTAGGGAGTGTAAGAAGTGATGGAAAATAGTACGACCGAAGCGCGTAATGAAGCGACGATGCATCTTGATGAAATGACTGTGGAAGAGGCTTTAATTACGATGAataaataa                                                                                                                                         >  1:356967/1‑141 (MQ=255)      aTGATACATTTGATTTTCAAAAAACTAGGGAGTGTAAGAAGTGATGGAAAATAGTACGACCGAAGCGCGTAATGAAGCGACGATGCATCTTGATGAAATGACTGTGGAAGAGGCTTTAATTACGATGAATAAATAAGATCa                                                                                                                                    >  1:42899/1‑141 (MQ=255)        gATACATTTGATTTTCAAAAAACTAGGGAGTGTAAGAAGTGATGGAAAATAGTACGACCGAAGCGCATAATTAAGCTACGATGCAACTTGATGAAATGACTGTGGAAGAGGCTTTAATTACGATGAATAAATAAGATCAGc                                                                                                                                  <  1:366186/141‑1 (MQ=255)         aTACATTTGATTTTCAAAAAACTAGGGAGTGTAAGAAGTGATGGAAAATAGTACGACCGAAGCGCGTAATGAAGCGACGATGCATCTTGATGAAATGACTGTGGAAGAGGCTTTAATTACGATGAATAAATAAGATCAGCa                                                                                                                                 <  1:451646/141‑1 (MQ=255)         aTACATTTGATTTTCAAAAAACTAGGGAGTGTAAGAAGTGATGGAAAATAGTACGACCGAAGCGCGTAATGAAGCGACGATGCATCTTGATGAAATGACTGTGGAAGAGGCTTTAATTACGATGAATAAATAAGATCAGCa                                                                                                                                 <  1:401606/141‑1 (MQ=255)          tACATTTGATTTTCAAAAAACTAGGGAGTGTAAGAAGTGATGGAAAATAGTACGACCGAAGCGCGTAATGAAGCGACGATGCATCTTGATGAAATGACTGTGGAAGAGGCTTTAATTACGATGAATAAATAAGATCAGCaa                                                                                                                                <  1:470295/141‑1 (MQ=255)                  aTTTTCAAAAAACTAGGGAGTGTAAGAAGTGATGGAAAATAGTACGACCGAAGCGCGTAATGAAGCGACGATGCATCTTGATGAAATGACTGTGGAAGAGGCTTTAATTACGATGAAAAAATAAGACCGGCAAGGCCCGtt                                                                                                                        >  1:173981/1‑141 (MQ=255)                     ttCAAAAACCTTGGGAGTGTAAGAAGTGATGGAAAATAGTACGACCGAAGCGCGTAATGAAGCGACGATGCATCTTGATGAAATGACTGTGGAAGAGGCTTTAATTACGATGAATAAATAAGATCAGCAAGTCCCGTTAGc                                                                                                                     <  1:200425/141‑1 (MQ=255)                          aaaaCTAGGGAGTGTAAGAAGTGATGGAAAATAGTACGACCGAAGCGCGTAATGAAGCGACGATGCATCTTGATGAAATGACTGTGGAAGCGGCATTAATTACGATGAATAAATAAGATCAGCAAGTCCCGTTAGCAGTTc                                                                                                                <  1:96396/141‑1 (MQ=255)                            aaCTAGGGAGTGTAAGAAGTGATGGAAAATAGTACGACCGAAGCGCGTAATGAAGCGACGATGCATCTTGATGAAATGACTGTGGAAGAGGCTTTAATTACGATGAATAAATAAGATCAGCAAGTCCCGTTAGCAGTTCGa                                                                                                              <  1:172082/141‑1 (MQ=255)                             aCTAGGGAGAGTAAGAAGTGATGGAAAATAGTACGACCGAAGCGCGTGATGAAGCGACGATGCATCTTGATGAGATGACTGTGGAAGAGGCTTTAATTACGATGAATAAATAAAATCAGCAAGTCCCGTTAGCAGTTCGaa                                                                                                             >  1:172748/1‑141 (MQ=255)                                       gtAAGAAGTGATGGAAAATAGTACGACCGAAGCGCGTAATGAAGCGACGATGCATCTTGATGAAATGACTGTGGAAGAGGCTTTAATTACGATGAATAAATAAGATCAGCAAGTCCCGTTAGCAGTTCGAAAGGCAATAcc                                                                                                   >  1:436814/1‑141 (MQ=255)                                            aagTGATGGAAAATAGTCAGAGACTAACGTTTAATGAAGCGACGATGCATCTTGATGAAATGACTGTGGACGAGGCTTTAATTACAATGAATAAATAAGATCAGCAAGTCCCGTTAGCAGTTCGAAAGGCAATACCACAAt                                                                                              >  1:119574/1‑141 (MQ=255)                                                  tGGAAAATAGTACGACCGAAGCGCGTAATGAGGCGACGATGCATCTTGATGAAATGACTGTGGAAGAGGCTTTAATTACGATGAATAAATAAGATCAGCAAGTCCCGTTAGCAGTTAGAAAGGCAATACCACAATTGACaa                                                                                        >  1:99311/1‑141 (MQ=255)                                                   ggAAAATAGTACGACCGAAGCGCGTAATGAAGCGACGATGCATCTTGATGAAATGACTGTGGAAGAGGCTTTAATTACGATGAATAAATAAGATCAGCAAGTCCCGTTAGCAGTTCGAAAGGCAATACCACAATTCACaaa                                                                                       >  1:417166/1‑141 (MQ=255)                                                                      gcgcGTAATGAAGCGACGATGCATCTTGATGAAATGACTGTGGAAGAGGCTTTAATTACGATGAATAAATAAGATCAGCAAGTCCCGTTAGCAGTTAGAAAGGCAATACCACAATTGACAAAAGTAATTAAAAAAACAAtt                                                                    >  1:470953/1‑141 (MQ=255)                                                                          gTAATGAAGCGACGATGCAACTTGATGAAATGACTGTGGAAGAGGCTTTAATTACGATGAATAAATAAGATCAGCAAGTCCCGTTAGCAGTTCGAAAGGCAATACCACAATTGACAAAAGTAATTAAAAAAACAATTGcac                                                                >  1:299249/1‑141 (MQ=255)                                                                             aTGAAGCGACGATGCATCTTGATGAAATGACTGTGGAAGAGGCTTTAATTACGATGAATAAATAAGATCAGCAAGTCCCGTTAGCAGTTCGACAGGCAATTCCTTAATTGACAAAAGTAATTAAAAAAACAATTGCACAGt                                                             <  1:219423/141‑1 (MQ=255)                                                                                    gacgaTGCATCTTGATGAAATGACTGTGGAAGAGGCTTTAATTACGATGAATAAATAAGATCAGCAAGTCCCGTTAGCAGTTCGAAAGGCAATACCACAATTGACAAAAGTAATTAAAAAAACAATTGCCAAGTCaaaaaa                                                      >  1:238418/1‑141 (MQ=255)                                                                                      cgaTGCATCTTGATGAAATGACTGTGGAAGAGGCTTTAATTACGATGAATAAATAAGATCAGCAAGTCCCGTTAGCAGTTCGAAAGGCAATACCACAATTGACAAAAGTAATTAAAAAAACAATTGCACAGTATAAAAAgg                                                    <  1:495492/141‑1 (MQ=255)                                                                                         tGCACCGTGATGAAATGACTGGGGAAGAGGCTTTAATTACGATGAATAAATAAGATCAGCAAGTCCCGTTAGCAGTTCGAAAGGCAAGACCACAATTGCCAAAAGTAATTAAAAAAACAATTGCACAGTATAAAAAGGGTg                                                 <  1:378118/141‑1 (MQ=255)                                                                                          gCACCTGGATGGAATGACTGTGGAAGAGGCTTTAATTACAATGAATAAATAAGATCAGCAAGTCCCGTTAGCAGTTCGAAAGGCAATACCACAACTGACAAAAGTAATTAAAAAAACAATTGCACAGTATAAAAAGGGTgg                                                <  1:488581/141‑1 (MQ=255)                                                                                            aTCTTGATGAAATGACTGTGGAAGAGGCTTTAATTACGATGAATAAATAAGATCAGCAAGTCCCGTTAGCAGTTCGAAAGGCAATACCACAATTGACAAAAGTAATTAAAAAAACAATTGCACACAATAAAAAGGGGGGAc                                              >  1:236642/1‑141 (MQ=255)                                                                                                              tgGAAGAGGCTTTAATTACGATGAATAAATAAGATCAGCAAGTCCCGTTAGCAGTTCGAAAGGCAATACCACAATTGACAAAAGTAATTAAAAAAACAATTGCACAGTATAAAAAGGGTGGACGATTGATTTATATCGGTg                            >  1:288732/1‑141 (MQ=255)                                                                                                                     ggCTTTAATTACGATGAATAAATAAGATCAGCAAGTCCCGTTAGCAGTTCGGAAGGCAATACCACTATTGACAAAAGTAATTAAAAAAACAATTGCACAGTATAAAAAGGGTCGACGATTGATTTATATCGGTGCAGGTAc                     >  1:347591/1‑141 (MQ=255)                                                                                                                        tttAATTACGATGAATAAATAAAAACCACTAGGCCCGTTAGCAGTTCGAAAGGCAATACCACAATTGACAAAAGTAATTAAAAAAACAATTGCACAGTATAAAAAGGGTGGACGATTGATTTATATCGGTGCAGGTACGAg                  >  1:368478/1‑141 (MQ=255)                                                                                                                               aCGATGAATAAATAAGATCAGCAAGTCCCGTTAGCAGTTCGAAAGGCAATACCACAATTGACAAAAGTAATTAAAAAAACAATTGCACAGTATAAAAAGGGTGGACGATTGATTTATATCGGTGCAGGTACAAGTGGAAgg           >  1:376765/1‑141 (MQ=255)                                                                                                                                      ataaataaGATCAGCAAGTCCCGTTAGCAGTTCGAAAGGCAATACCACAATTGACAAAAGTAATTAAAAAAACAATTGCACAGTATAAAAAGGGTGGACGATTTATTTATATCGGTGCAGGTACAAGTGGAAGGTTGGgtg    >  1:11994/1‑141 (MQ=255)                                                                                                                                      ataaataaGATCAGCAAGTCCCGTTAGCAGTTCGAAAGGCAATACCACAATTGACAAAAGTAATTAAAAAAACAATTGCACAGTATAAAAAGGGTGGACGATTGATTTATATCGGTGCAGGTACAAGTGGAGGGTTGGgtg    >  1:453409/1‑141 (MQ=255)                                                                                                                                        aaaTAAGATCAGCAAGTCCCGTTAGCAGTTCGGAAGGCAATACCACAATTGACAAAAGTAATTAAAAAAACAATTGCACAGTATAAAAAGGGTGGGCGATTGAGTTATATCGGTGCAGGTACAAGTGGAAGGTTGGgtgta  >  1:105670/1‑140 (MQ=255)                                                                                                                                           |                                                                                                                                          GCCGAATGATACATTTGATTTTCAAAAAACTAGGGAGTGTAAGAAGTGATGGAAAATAGTACGACCGAAGCGCGTAATGAAGCGACGATGCATCTTGATGAAATGACTGTGGAAGAGGCTTTAATTACGATGAATAAAGAAGATCAGCAAGTCCCGTTAGCAGTTCGAAAGGCAATACCACAATTGACAAAAGTAATTAAAAAAACAATTGCACAGTATAAAAAGGGTGGACGATTGATTTATATCGGTGCAGGTACAAGTGGAAGGTTGGGTGTC  >  USA300TCH1516_ALE/224866‑225141

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑